title: Transcriptional analysis of maize leaf tissue treated with seaweed extract under drought stress

city: Bhavnagar

first: Khanjan

last: Trivedi

state: Gujarat

address: GB Marg

department: AP&BD

country: India

institute: CSIR-Central Salt & Marine Chemical Research Institute

summary: Kappaphycus alvarezii seaweed extract (KSWE) has been known for its plant biostimulant and stress alleviation activities on various crops. However, very few reports are available depicting its impact at the molecular level, which is crucial in identifying the mechanism of action of KSWE on plants. Here, maize leaf tissue of control and KSWE treated plants were analyzed for their transcriptional changes under drought stress. KSWE was applied foliarly at the V5 stage of maize crop under drought and leaf transcriptome analysis was performed. It was found that total of 380 and 631 genes were up- and down- regulated, respectively due to the application of KSWE. Genes involved in nitrate transportation, signal transmission, photosynthesis, transmembrane transport of various ions, glycogen and starch biosynthetic processes were found up-regulated in KSWE treated plants. While genes involved in the catabolism of polysaccharide molecules such as starch as well as cell wall macromolecules like chitin and protein degradation were found down-regulated. An overview of differentially expressed genes involved in metabolic as well as regulatory processes in KSWE treated plant was also analyzed via Mapman tool. Phytohormone signaling genes such as cytokinin-independent 1 (involved in cytokine signal transduction), Ent-kaurene synthase and GA20 oxidase (involved in gibberellin synthesis) and gene of 2-oxoglutarate-dependent dioxygenase enzyme activity (involved in ethylene synthesis) were found up-regulated while 9-cis-epoxycarotenoid dioxygenase (a gene involved in abscisic acid synthesis) was found down regulated due to the application of KSWE. Modulation of gene expression in maize leaf tissue  in response to KSWE treatment elucidate mechanisms to ward off drought stress which can be extended to understand similar phenomenon in other crops as well. . This molecular knowledge can be utilized to make the use of KSWE more efficient and sustainable.

overall_design:
Two samples (prepared by pooling three indipendent samples) were analyzed with two technical replicates. Among them one is control and one is treated sample.
**Raw data not provided**

first: KG

last: Vijayanand

first: Ranjeet

last: Kumar

first: Arup

last: Ghosh*


title: Antisense RNAs influence promoter usage of their counterpart sense genes in cancer

status: Public on Nov 15 2021

city: Singapore

first: Polly Leilei

last: Chen

address: #12-01, MD6, 14 Medical Drive

department: Department of Anatomy

country: Singapore

institute: Cancer Science Institute of Singapore NUS

summary: Natural antisense transcripts (NATs) are those RNAs transcribed from the same locus, but in the opposite direction to a sense gene transcript. non-coding NATs (ncNATs) have been reported to modulate key biological events such as cell differentiation and carcinogenesis through gene expression regulation; nevertheless, their actual impact on cancer remains largely unknown. Due to their low expression levels and their overlap with sense genes, the study of ncNATs using RNA-seq is challenging. Public databases frequently register incomplete sequences of ncNATs, and mostly in a not tissue-specific manner. In the present study, we aim to better characterize the nature of ncNATs expressed in liver and hepatocellular carcinoma (HCC). For that, we performed strand-specific RNA-seq in 6 pairs of HCC - normal adjacent liver tissues from 6 HCC patients. Knowing the strand origin of the reads, we will be able to determine the actual nature and span of those ncNATs expressed in the liver and in HCC.

overall_design: We constructed strand-specific cDNA libraries of 12 total RNA samples, corresponding to six paired sets of HCC and normal adjacent liver tissues.

first: Chen

last: Leilei

first: Fernando

middle: B

last: Molias

first: Yangyang

last: Song

first: Omer

last: An


title: Next generation sequencing identifies paraneoplastic effects of tumor-derived FGF19 on murine liver transcriptomes

city: Orlando

first: Deborah

last: Altomare

state: FLORIDA

address: 6900 Lake Nona Blvd.

department: Cancer Research

country: USA

institute: University of Central Florida

type: Expression profiling by high throughput sequencing

summary:
Purpose. Despite having excellent prognosis when detected early, colorectal cancer (CRC) remains a leading cause of cancer-related deaths globally. Barriers to screening reduces compliance and negatively impacts patient outcomes, necessitating alternatives. A blood-based approach provides a more convenient and accessible modality, but serum markers are lacking. Using a meta-transcriptomics approach, we identified Fibroblast Growth Factor 19 (FGF19), an enteroendocrine FGF responsible for bile acid (BA) homeostasis, as an attractive CRC marker. However, whether FGF19 is aberrantly secreted into blood by colorectal tumors or induces endocrine-like paraneoplastic effects is unknown.
Methods. To test if colorectal tumors contribute FGF19 into blood, subcutaneous xenografts of HCT116 and Colo201 cells were established in four male and female NSG mice. Tumor volume, as well as serum and urine FGF19 were assessed over 36 days. Following euthanasia, murine liver was processed for downstream mRNA and bile acid quantification. To determine global paraneoplastic effects of malignant FGF19 on its primary target organ (liver), hepatic mRNA was isolated and subjected to RNA sequencing on an Illumina NovaSeq 6000 system. Reads were processed, aligned, mapped, and analyzed for differential expression and functional enrichment using an integrated informatics pipeline implemented in R.
Results. Circulating FGF19 levels derived from subcutaneous xenografts of Colo201, but not HCT116, cells exerted paraneoplastic effects on liver including suppression of BA synthesis, dysregulation of cholesterol metabolism, and induction of pre-neoplasia.
Conclusion. Here we report novel paraneoplastic effects of tumor derived FGF19 on liver tissue. Study limitations include in vivo experimentation using two different cell lines, and significant gender-related batch effects in RNA sequencing data.

overall_design: Examination of liver transcriptomes from mice harboring subcutaneous xenografts of FGF19-Lo (HCT116) and FGF19-Hi (Colo201) expressing Colorectal cancer cell lines

first: Michael

last: Rohr


title: Dietary palmitic acid promotes a prometastatic epigenetic memory related to tumor innervation

status: Public on Nov 16 2021

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

country: Spain

institute: Parc Taulí Research and Innovation Institute (I3PT)

type: Genome binding/occupancy profiling by high throughput sequencing

summary: This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: An IL-9-pulmonary macrophage axis defines the allergic lung inflammatory environment

city: Indianapolis

first: Yongyao

last: Fu

state: IN

address: 635 Barnhill Drive, MS 218

department: Microbiology and Immunology

institute: Indiana University

summary: Despite IL-9 functioning as a pleiotropic cytokine in mucosal environments, the IL-9 responsive cell repertoire is still not well defined. Here, we found IL-9 mediates pro-allergic activities by targeting lung macrophages. IL-9 inhibits alveolar macrophage expansion and promotes recruitment of monocytes that develop into CD11c+/- interstitial macrophage populations. Interstitial macrophages were required for IL-9-dependent allergic responses. Mechanistically, IL-9 affects the function of lung macrophages by inducing Arg1 activity. Compared to Arg1-deficient lung macrophages, Arg1-expressing macrophages co-express greater amounts of CCL5. Adoptive transfer of Arg1+ lung macrophages but not Arg1- lung macrophages can recover allergic inflammation that is lost in Il9r-/- mice. In parallel, the elevated expression of IL-9, IL-9R, Arg1 and CCL5 is correlated with disease in asthma patients. Thus, our study uncovers an IL-9/macrophage/Arg1 axis as a potential therapeutic target for allergic airway inflammation.

overall_design: There are two samples, one is  pooled cells of WT lung macropahges and WT blood monocytes, the other one is pooled cells of Il9r KO lung macropahges and Il9r KO blood monocytes.

first: Mark

middle: H

last: Kaplan

first: Hongyu

last: Gao


title: RNAsequencing of control and STAT3 knocked down transriptomes of EndoC cells

city: Anderlecht

first: Valerie

last: Vandenbempt

state: Vlaams-Brabant

address: Lenniksebaan 808

country: Belgium

institute: Université Libre de Bruxelles

summary: Most obese and insulin resistant individuals do not develop diabetes. This is the result of the capacity of β-cells to adapt and produce enough insulin to cover the needs of the organism. The underlying mechanism of β-cell adaptation in obesity, however, remains unclear. Previous studies have suggested a role for STAT3 in mediating β-cell development and human glucose homeostasis, but little is known about its role in β-cells in obesity. We observed enhanced cytoplasmatic expression of STAT3 in severe obese and diabetic subjects. To address the functional role of STAT3 in adult β-cells, we generated mice with tamoxifen-inducible partial or full deletion of STAT3 in β-cells and fed them a high fat diet before analysis. Interestingly, β-cell homozygous and heterozygous STAT3 deficient obese mice showed glucose intolerance when compared to controls. Gene expression analysis by RNA-seq showed reduced expression of mitochondrial genes in STAT3 knocked-down human EndoC-βH1 cells and was confirmed in FACS-purified β-cells from STAT3 deficient mice. Moreover, knockdown of STAT3 impaired mitochondria activity in EndoC-βH1 and human islets, suggesting a mechanism for STAT3-regulated β-cell function. We propose non-canonical STAT3 activity as a marker of β-cell identity, improving glucose induced insulin secretion in obesity.

overall_design: mRNA profiles of control and STAT3 knocked-down β-cells

first: Anais

last: Schaschkow

first: Lokman

last: Pang

first: Bernat

last: Elvira

first: Sara

middle: A

last: Litwak

first: Beata

last: Vekeriotaite

first: Elisa

last: Maillard

first: Flavia

middle: M

last: Paula

first: Piero

last: Marchetti

first: Daniel

middle: J

last: Gough

first: Esteban

middle: N

last: Gurzov


title: Intestinal epithelial GR in response to DEX treatment

city: Durham

first: Jian-Liang

last: Li

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

summary: The goal of this project is to investigate the role of glucocorticoids and their receptor, glucocorticoid receptor (GR) , in intestinal stress response and tissue homeostasis.We generated a mouse model with specific deletion of GR in intestinal epithelium (GR iKO mice) and examined colonic transcriptomes of adrenalectomized (ADX) Flox control and GR iKO mice in response to dexamethasone (DEX) treatment by microarray analysis.

overall_design: Total RNA were extracted from colon tissues of 4 pairs adrenalectomized (ADX) Flox control and GR iKO mice treated with or without 1 mg/Kg dexamethasone (DEX) for 6 hours.  Gene expression profiles were analyzed using Agilent Whole Mouse Genome 4x44 multiplex format oligo arrays (014868) (Agilent Technologies, Santa Clara, CA), following the Agilent 1-color microarray-based gene expression analysis protocol.

first: Xiaoling

first: Shuang

last: Tang


title: Topoisomerases I and II facilitate the translocation of condensin DC in C. elegans [ChIP-seq]

status: Public on Nov 14 2021

city: New York

first: Ana

middle: Karina

last: Morao

state: New York

address: 29 Washington Place

department: Biology

institute: New York University

summary: Condensin complexes are evolutionarily conserved molecular motors from the structural maintenance of chromosomes (SMC) family, that use ATPase activity to translocate along DNA and form loops. Condensin and topoisomerase II (TOP-2) are essential for the structure and function of mitotic chromosomes. While condensin-mediated DNA looping is thought to direct TOP-2 chain-passing activity to separate sister chromatids, it is not known if TOP-2 in turn regulates loop formation. Here we used an X chromosome specific condensin that represses transcription for dosage compensation in C.elegans, to determine how DNA topology affects SMC translocation in vivo. We applied auxin-inducible degradation of topoisomerases I and II to determine their effect on condensin DC binding and function. We found that both topoisomerases colocalize with condensin DC and control its movement at different genomic scales. TOP-2 depletion hindered condensin DC spreading over long distances, resulting in accumulation around its X-specific recruitment sites and shorter Hi-C interactions. In contrast, TOP-1 depletion did not affect long-range spreading but resulted in accumulation of condensin DC within gene bodies, specially of highly expressed and long genes. Both TOP-1 and TOP-2 depletion resulted in X chromosome upregulation indicating that condensin DC translocation at both scales is required for its function in transcriptional repression. Together our work reveals distinct DNA topological requirements for two modes of condensin DC association with chromatin: long-range linear translocation that requires decatenation and unknotting of DNA and short-range binding to genes that requires resolution of transcription-induced supercoiling.

sample_organism:
Caenorhabditis briggsae
Caenorhabditis elegans

overall_design: ChIP-seq data in WT, controls and topoisomerases I and II depleted conditions . Depletion was performed by Auxin inducible degradation. All experiments were performed in two biological replicates. L2/L3 larvae were used for most experiments. TOP-2 ChIP-seq in embryos and adults are also included.

middle: K

first: Jun

last: Kim

last: Obaji

first: Siyu

last: Sun

first: Sevinc

last: Ercan


title: Brain transcriptome analysis of a TPP-1 neuronal ceroid lipofuscinosis mouse model as disease progresses

city: Chicago

first: Miriam

middle: S.

last: Domowicz

state: Illinois

address: 5841 S Maryland Ave MC5058

department: Pediatrics

institute: University of Chicago

summary: We analyzed expression changes in the Tpp1-/- forebrain/midbrain and cerebellum of 1, 2, and 3 mo. mutants compared to strain-related controls RNA-sequencing technology.

overall_design: The objective of this study was to perform a transcriptome wide characterization by RNA-seq of two affected brain-areas (cerebellum (Cb) and forebrain/midbrain (F/M)) at 1-, 2- and 3-mo.-old Tpp1-/-  compared to age matched wild type siblings.  We used a mouse model previously developed by the Lobel laboratory (J. Neurosci. 2004, 24(41)9117).

middle: S

first: Wen-Ching

last: Chan

first: Patricia

last: Claudio-Vázquez

first: Tatiana

last: Gonzalez

first: Nancy

last: Schwartz


title: Anti-leukemia activity of bortezomib through GATA2-WT1 axis in acute myeloid leukemia

city: Wenzhou

first: Jinglai

last: Dong

address: Life and healthy town

country: China

institute: The First Affiliated Hospital of Wenzhou Medical University

summary: GATA2 is a transcription factor essential for hematopoietic differentiation and lymphatic system formation.  High expression of GATA2 has been implicated in myelodysplastic syndrome and acute myeloid leukemia. Bortezomib  has a good effect in MM. However, the mechanism of bortezomib possesses anti-self-renewal and leukemogenesis in AML is still unclear. Here, we reported that GATA2 and WT1 protein is degraded by bortezomib. The half-life of GATA2 mRNA was obviously shorter in Bortezomib-treated cells. Knockdown of GATA2 by small hairpin RNAs (shRNAs) has potential anti-leukemia activity in leukemic cells. Bortezomib inhibited cell proliferation and induced apoptotic death without activation of caspases pathway. Finally, bortezomib decreased xenograft tumor size in a xenograft leukemia mouse model, and prolonged the survival time in mouse C1498 AML model. Collectively, bortezomib might be a potential treatment for AML.

overall_design: RNA sequencing from K562 cells treated with or without bortezomib

first: Bin

last: Zhou

first: Haige

last: Ye

first: Chongyun

last: Xing

last: Liang

first: Xingzhou

last: Huang

first: Yanfei

last: Wu

first: Shenmeng

last: Gao


title: Transcriptome of new DROSHA_KO mouse embryonic stem cells generated by paired CRISPR/Cas9 approach

city: Zurich

first: Constance

last: Ciaudo

state: Zurich

address: Otto-Stern-Weg 7, HPL G.31

country: Switzerland

institute: ETH Zurich

summary: Purpose:  The goals of this study was to obtain the trasncriptome of DROSHA_KO mESCs to compare it with the transcriptome of WT mESCs (originally deposited in GSE78971 and included here).

overall_design:
mRNA profiles of DROSHA_KO mouse embryonic stem cells were generated by deep sequencing, in duplicate, using Illumina HiSeq2000.

Two independent knockout strategies were used and each is represented in a separate sample:

GSM3476626 DroshaKO1d5_A with deletion of Pro-rich region
GSM3476627 DroshaKO2d5_B with deletion of R/S-rich region

The Drosha KO alleles are discussed in PubMed ID: 28100686


title: Merkel cell formation in hairy and glabrous skin

city: New Haven

first: Dejian

last: Zhao

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale School of Medicine

summary: We describe Merkel cell formation in glabrous skin during embryogenesis. In our study, we first found that Merkel cells were specified at E15.5, 24 hours later, comparing to the back skin. Interestingly, by performing lineage-tracing experiments, we found that unlike back skin, SOX9(+) cells do not give rise to Merkel cells in glabrous skin. We performed transcriptional profiling of Merkel cells of the back and glabrous skin and showed that their transcriptoms are very similar. Taken together, Merkel cells in back skin and glabrous skin are similar, and their formation is controlled by a common genetic program, although their precursor cells might differ.

overall_design: P0 mouse epidermal cells and Merkel Cell at back skin and paw  were purified from Atoh1-GFP mice. RNA from the sorted cells was analyzed by RNA-seq.

first: Minh

last: Nguyen

first: Victor

last: Valdes

first: Idan

last: Cohen

first: Deyou

last: Zheng

first: Elena

last: Ezhkova


title: Comparing gene expression across primary human airway models for cystic fibrosis precision medicine

city: Toronto

first: Gengming

last: He

address: 27 King's College Circle

department: Biostatistics

country: Canada

institute: University of Toronto

summary:
Rationale:Cultured human bronchial epithelia (HBE) are the gold standard model for assessing the efficacy of small molecule therapies in cystic fibrosis (CF). However, these cells are difficult to access, especially in young children. Human nasal epithelia (HNE) are used as a surrogate model although it is unknown whether HNE recapitulate the gene expression properties of HBE
Objective: To investigate the similarities and differences in gene expression genome-wide between HBE and HNE with a focus on CF lung disease modifier genes.
Methods: RNA-sequencing was conducted on paired cultured and naïve HNE and HBE (n=71 samples) collected from 21 patients with CF who underwent lung transplantation. Gene expression was first compared across cultured and naïve samples to assess the impact of the culturing process, then compared between cultured HNE and HBE. Co-expression relationships of CF modifier genes were compared between cultured HNE and HBE.
Results: The culturing process had little impact on the expression level of CF lung disease modifier genes. These genes also showed significant equivalent expression between cultured HNE and HBE. Their co-expression relationships in cultured HNE and HBE overlapped significantly, suggesting the corresponding biological processes are consistent across the two tissues.
Conclusions: CF lung disease modifier genes have similar expression profiles across cultured HNE and HBE.  This supports the use of HNE as a surrogate airway model to investigate CF lung disease, modifier genes and enable investigation of CF precision medicine.

overall_design: mRNA profile of paired human bronchial epithelia (HNE) and human nasal epithelia (HBE), cultured and uncultured

first: Tanja

last: Gonska

first: Theo

last: Moraes

first: Lisa

last: Strug


title: The circular RNA profiling of 10 paired HCC and matched peritumor tissues

status: Public on Nov 13 2021

city: Fuzhou

first: Liman

last: Qiu

address: Xihong Road 312, Fuzhou 350025, Fujian, P. R. China.

institute: Mengchao Hepatobiliary Hospital of Fujian Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: We collected primary HCC tumor and matched peritumor tissues from 10 HBV-related HCC patients to analyze the circRNA profile and its alteration in HCC through RNA-seq. A total of 92,204 circRNAs were identified in these 20 tissue samples with more than two unique back-spliced reads, of which 42 circRNAs were dysregulated in all HCC tumor tissue samples when compared with matched peritumor tissues (fold change≥2 and p<0.05). As the detailed analysis of circRNA profiles in HCC, our study  undoubtedly improved the comprehensiveness of HCC associated circRNA profiles.

overall_design: Examination of 10 paired HCC and matched peritumor tissues

first: Zhenli

last: Li

first: Zhixiong

last: Cai

first: Xiaolong

last: Liu


title: A three lncRNA set: AC009975.1, POTEH-AS1 and AL390243.1 as nodal efficacy biomarker of neoadjuvant therapy for HER-2 positive breast cancer

city: Jinan

first: Zhao

last: Bi

address: Jiyan Road 440

institute: Shandong Cancer Hospital

summary: We explored whether lncRNA expression in primary tumor had nodal predicting value for HER-2 positive breast cancer who received neoadjuvant therapy. To explore the differentially expressed lncRNA, six HER2+ fresh core biopsies tissues before NAT were collected (3 tissues from ypT0N0 group and 3 tissues from ypT+N+ group) and subjected to lncRNA microarray. Different lncRNAs (POTEH-AS1, LncRNA-AL390243.1, and lncRNA-AC009975.1 ) were selected by microarray, validated by qPCR,

overall_design: Gene expression in core biopsies tissues was measured from patients with ypT0N0 and ypT+N+ subtype.

first: Yong-Sheng

last: Wang

first: Xian-Rang

last: Song


title: A Single Human-Relevant Fast Food Meal Produces Rapid Reorganization of the Gut Microbiome Revealing Unique Gut Microbe-Dependent Metabolomic Signatures

city: Cleveland

first: Lucas

last: Osborn

state: Ohio

address: 9500 Euclid Ave

institute: Cleveland Clinic Foundation

summary: Background: More than 100 million Americans are living with metabolic syndrome, increasing their propensity to develop heart disease– the leading cause of death worldwide. A major contributing factor to this epidemic is caloric excess, often a result of consuming low cost, high calorie fast food. Several recent seminal studies have demonstrated the pivotal role of gut microbes contributing to cardiovascular disease in a diet-dependent manner. Given the central contributions of diet and gut microbiota to cardiometabolic disease, we hypothesized that novel microbial metabolites originating postprandially after fast food consumption may contribute to cardiometabolic disease progression. Methods: To test this hypothesis, we gave conventionally raised or antibiotic-treated mice a single oral gavage of a fast food slurry or a control rodent chow diet slurry and sacrificed the mice four hours later. Here, we coupled untargeted metabolomics in portal and peripheral blood, 16S rRNA gene sequencing, targeted liver metabolomics, and host liver RNA sequencing to identify novel fast food-derived microbial metabolites. Results: We successfully identified several metabolites that were enriched in portal blood, increased by fast food feeding, and essentially absent in antibiotic-treated mice. Strikingly, just four hours post-gavage, we found that fast food consumption resulted in rapid reorganization of the gut microbial community structure and drastically altered hepatic gene expression. Importantly, diet-driven reshaping of the microbiome and liver transcriptome was dependent on a non-antibiotic ablated gut microbial community. Conclusions: Collectively, these data suggest that single fast food meal is sufficient to reshape the gut microbial community yielding a unique signature of food-derived microbial metabolites. Future studies are warranted to determine if these metabolites are causally linked to cardiometabolic disease.

overall_design: Comparison of liver mRNA transcription profiles after oral gavage of fast food or chow slurries in control or antibiotic treated mice. N=4 per group.

first: Danny

last: Orabi


title: Human liver cancer cells Hep3B: Valeric acid treated vs. Control

status: Public on Nov 12 2021

first: Yong

last: Zhu

address: 60 College Street

institute: Yal University

summary: Transcriptional profiling of human liver cancer cells (Hep3B) treated with valeric acid compared to control.

overall_design: Two-condition experiment, valeric acid vs.control. Biological replicates: 3 valeric treated, 5 controls from 2 batches, independently grown and harvested. One replicate per array.


title: Diverse epigenetic mechanisms maintain parental imprints within the embryonic and extraembryonic lineages

city: Munich

first: Daniel

last: Andergassen

address: Biedersteiner Straße 29

country: Germany

institute: Technical University Munich

type: Methylation profiling by high throughput sequencing

summary: Genomic imprinting and X chromosome inactivation (XCI) require epigenetic mechanisms to direct allele-specific expression. Despite their critical roles in embryonic development, how universal epigenetic regulators coordinate these specific tasks at single loci or across chromosome scales remains understudied. Here, we systematically disrupted essential epigenetic pathways within polymorphic F1 embryos to examine canonical and non-canonical genomic imprinting as well as X chromosome inactivation. We find that DNA methylation and Polycomb group repressors are both indispensable for autosomal imprinting, albeit at distinct gene sets. Moreover, the extraembryonic ectoderm relies on a broader spectrum of imprinting mechanisms, including non-canonical targeting of maternal endogenous retrovirus (ERV) driven promoters by the H3K9 methyltransferase G9a. We further utilize our data to identify Polycomb dependent and independent gene clusters on the imprinted X chromosome, which appears to reflect distinct domains of Xist-mediated suppression. From our data, we assemble a comprehensive inventory of the epigenetic mechanisms utilized in eutherian mammals to maintain parent-specific imprinting, including an expanded view of the placental lineage that comprises multiple unique pathways.

overall_design: For this study, we disrupted the DNA methyltransferase Dnmt1, the histone 3 lysine 9 (H3K9) methyltransferases G9a and Glp (target genes Ehmt1 and Ehmt2, double KO), as well as the PRC1 and PRC2 complexes individually (target genes: Rnf2 and Eed, respectively) in BDF1xCAST zygotes. Epiblast and ExE samples were collected from 30 knockout embryos on E6.5 and processed for bulk RNA sequencing.

first: Zachary

middle: D

last: Smith

first: Helene

last: Kretzmer

first: John

middle: L

last: Rinn

first: Alexander

last: Meissner


title: RNA-seq of wild-type and ∆yhdJ Salmonella enterica serovar Typhimurium (14028s)

city: Boston

first: Jeffrey

last: Bourgeois

address: 136 Harrison Ave

institute: Tufts University

summary: An RNA-seq analysis of wild-type Salmonella enterica serovar Typhimurium and ∆ydhJ isogenic mutant grown under SPI-1-inducing and SPI-2-inducing conditions.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: RNA-seq on 3 independent replicates of wild-type or ∆yhdJ S. Typhimurium

first: Dennis

middle: C

last: Ko


title: RNA-seq of wild-type and ∆metJ Salmonella enterica serovar Typhimurium (14028s)

summary: An RNA-seq analysis of wild-type Salmonella enterica serovar Typhimurium and ∆metJ isogenic mutant grown under SPI-1-inducing and SPI-2-inducing conditions.

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: RNA-seq on 3 independent replicates of wild-type or ∆metJ S. Typhimurium


title: Transcriptomics of vitiligo melanocytes after hydroxychloroquine treatment

city: Hangzhou

first: Bo

last: Xie

address: Westlake Road, 38

institute: Hangzhou Third People's Hospital, Affiliated Dermatology Hospital of Zhejiang University School of Medicine

summary:
Purpose: In order to explore the mechanism of hydroxychloroquine (HCQ) in treating vitiligo. We report the application of transcriptome profiling (RNA-seq) in human vitiligo melanocytes cell line PIG3V after HCQ treatment.
Methods: The PIG3V cells were divided randomly in two groups: HCQ treatment (1 μg/mL, 24 hours) and the cells without treatment (only medium). RNA samples extracted from PIG3V cells were quantified by NanoDrop  and Bioanalyzer. After 2 rounds of purification Poly A RNA was extracted then from total RNA by using Dynabeads Oligo. Small pieces of Poly A RNA were returned through Magnesium RNA Fragmentation Module under the condition of 94℃ for 5 minutes. Subsequently, SuperScript Reverse Transcriptase was used to reverse-transcribe the cleaved RNA pieces into cDNA. Then, U-labeled second-stranded DNAs was synthesized. After adding of A-base to each strand, preparing for indexed adapters, and heat-labile UDG enzyme treatment, PCR amplification was performed under (1) 95℃, 3 minutes; (2) 98℃, 15 seconds for 8 cycles; (3) 60℃, 15 seconds, 72℃, 5 minutes. Ultimately, RNA sequencing was performed according to protocol of Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China). After calculation, differential expressed genes were screened by fold change (FC)＞2 or FC＜0.5 and p value＜0.05.
Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample and identified 60612 genes and 229420 transcripts. Approximately 0.3% of the genes showed differential expression between the HCQ treated PIG3V cells and the cells without HCQ, with a fold change＞2 or＜0.5 , p value＜0.05.
Conclusions: Our research showed the first detailed transcriptome analysis of human vitiligo melanocytes PIG3V, with or without HCQ treatment. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic mechanisms of HCQ in treating vitiligo.

overall_design: mRNA profiles of human vitiligo melanocytes PIG3V treated by hydroxycholoroquine, and PIG3V group without hydroxycholoroquine treatment

first: Xiuzu

first: Yi

last: Chen

first: Yebei

last: Hu


title: Mechanical Stiffness Controls Dendritic Cell Metabolism and Function

city: Novato

last: Winer

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

summary: Impact of static mechanical tension on global gene expressison in dendritic cell culture

overall_design: Stiffness in the tissue microenvironment changes in most diseases and immunological conditions, but its direct influence on the immune system is poorly understood. Here, we sought to understand how static mechanical tension impacts global gene transcriptional changes across bulk cell types generated by traditional bone marrow dendritic cell culture methods.  We cultured bone marrow derived dendritic cells at both low tension, reminiscent of physiological stiffness (2kPa), as well as at stiffness seen more in fibro-inflammatory disease (50kPa).  This work identified numerous genes and transcriptional programs modulated by environmental stiffness across myeloid populations within a dendritic cell bone marrow culture and identifies stiffness as a critical modulator of genetic programs in the innate immune system

first: Mainak

last: Chakraborty

first: Annie

last: Shrestha

first: Xavier

last: Revelo

first: Sue

last: Tsai


title: A comparative transcriptome and chromatin modification analysis provides a resource for characterizing the regulatory roles of epigenetic modifications in hulless barley resistance response to powdery mildew

city: Wuhan

first: Zhou

last: Jian

address: Wuhan China

institute: AJBK

summary: We generated  ChIP-Seq data for two barley accessions with different resistance to powdery mildew. These data allowed us to explore the roles of epigenetic modifications in resistance response to powdery mildew at the first time. Our study opens the way for establishing the relationship between epigenetics and disease response in barley, and should inform future functional characterization of the regarding molecular basis. These data should also help researchers to exploit disease response-related genes for breeding application.

overall_design: Examination of 2 different histone modifications (H3K27ME3, H3K4ME3) in 2 hulless barley varieties sprayed with white powder bacteria and collected at different time points (0h, 6h, 36h, 72h, 168h).

first: Mingzhai

last: Yu

first: Yulin

last: Wang

first: Zeqing

last: Li

first: Xingquan

last: Zeng

first: Hongjun

last: Yuan

first: Qijun

last: Xu

first: Sang

last: Za

first: Tashi

last: Nyima


title: PacBio SMRT-seq of wild-type, ∆metJ, and ∆dam Salmonella enterica serovar Typhimurium (14028s)

first: Jeffrey

last: Bourgeois

summary: PacBio SMRT-seq of wild-type, ∆metJ, and ∆dam Salmonella enterica serovar Typhimurium grown under SPI-1-inducing and SPI-2-inducing conditions.

overall_design: SMRT-seq performed on 1 biological replicate

first: Dennis

last: Ko


title: PacBio SMRT-seq of wild-type, ∆metJ, and ∆yhdJ Salmonella enterica serovar Typhimurium (14028s)

summary: PacBio SMRT-seq of wild-type, ∆metJ, and ∆yhdJ Salmonella enterica serovar Typhimurium grown under SPI-1-inducing condition.

first: Bourgeois

last: Jeffrey

first: Ko

last: Dennis


title: Dlx1/2-Dependent Expression of Meis2 Promotes Neuronal Fate

city: Shanghai

first: Zihao

last: Su

address: 138 Yi Xue Yuan Road

institute: Fudan University

summary: To acess chromatin accessibility of individual cell from  striatum of E14.5 wild type mice.

overall_design: Individual cells were sampled from mice striatum of E14.5 wild type mice

first: Ziwu

first: Zhuangzhi

last: Zhang

first: Lin

last: Yang


title: Pathway-focused (Ostegenesis) gene expression analysis of healthy, injured and treated rat entheses samples

status: Public on Nov 11 2021

city: Maastricht

first: Carlos

middle: Julio

last: Peniche Silva

state: Limburg

address: Universiteitssingel 40

department: cBITE

country: Netherlands

institute: MERLN/Maastricht University

summary: In the present study, a defect was created in the patellar enthesis of a rat model, and treatment was provided using two versions of a biphasic silk fibroin scaffold showing two different transition morphology between the phases.  The study included two scaffold-treated groups, two control groups, and one native/healthy group. For the scaffold-treated groups, the defect was treated by implanting one of the two versions of the biphasic scaffolds. One scaffold showed a mixed/interconnected transition zone between the tendon and bony part of the construct (S-MT) while the transition in the other scaffold was abrupt (S-AT). Two control groups were included. In the first group, a defect was created in the patellar enthesis and the tendon was sutured back over the defect and to the bone. In the second group, a transversal cut was performed at the tendon part of the enthesis and sutured back. Samples were collected (n=8) per group at two time points (4 weeks and 12 weeks) after the surgery. Healthy (contralateral) samples were used as reference. The Qiagen Osteogenesis Pathway-focused PCR array was utilized to profile the expression of relevant osteogenic, chondrogenic, and tenogenic genes in samples from healthy, injured and treated patellar entheses samples.

overall_design: A total of 72 samples were used in the study. 8 samples per group and time point and 8 samples of healthy enthesis as reference.

first: Martijn

last: van Griensven

first: Elizabeth

middle: R

last: Balmayor


title: Next Generation Sequencing Facilitates Quantitative Analysis of LPS treated THP-1 cells' Transcriptomes

city: Charleston

first: Zhenwu

last: Luo

state: SC

address: 173 Ashley Ave

department: Immunology & Microbiology

institute: Medical University of South Carolina

summary: In order to understand the consequences of the LPS from different bacterias, we analyzed RNA gene expression profiles in a human myeloid cell line THP-1 cells. RNA-seq transcriptome was analyzed in THP-1 cells treated with LPS from three bacteria B. fungorum, S. marcescens, and P. myrsinacearum.

overall_design: mRNA profiles of bacteria B. fungorum, S. marcescens, and P. myrsinacearum LPS treated THP-1 cells

first: Wei

last: Jiang


title: Whole Transcript Expression Array Analysis of Human Colon Fibroblasts Culture Treated with Helichrysum italicum Infusion

city: Izola

first: Sasa

last: Kenig

address: Polje 42

department: Faculty of Health Sciences

country: Slovenia

institute: University of Primorska

summary:
Helichrysum italicum (HI) is a Mediterranean plant with well-reported use in traditional medicine for a wide range of applications, related mostly to respiratory, digestive and dermatologic conditions. The health-beneficial potential of H. italicum has been supported by numerous in vitro and in vivo experiments, however, little is known about the global mechanism behind its pleiotropic activity.
The aim of this study was to enhance the understanding of the potential biological processes induced in primary colon fibroblasts by HI infusion exposure for 6 h and 24 h, using a microarray-based transcriptome analysis. Altogether we identified 217 differentially expressed genes compared to non-treated cells, and only 8 were common to both treatments. Gene ontology analysis revealed that 24 h treatment with HI infusion altered the expression of genes involved in cytoskeleton rearrangement and cell growth, whereas pathway analysis further showed the importance of interleukin signaling and transcriptional regulation by TP53. For the 6 h treatment only the process of hemostasis appeared in the results of both analyses. With the careful evaluation of the role of individual genes represented in the enriched pathways and processes, we propose the main mode of HI action, which is wound healing. In addition to its indirect prevention of diseases resulting from impaired barrier integrity, HI also effects inflammation and metabolic processes directly.

overall_design: Primary colon fibroblasts (CCD122CoN) were chosen as a cell model for testing the intestinal activity of HI infusion, since colonic subepithelial fibroblasts are known to contribute to the maintenance of epithelial cell homeostasis, wound healing, and immune responses. 24 h after seeding, CCD122CoN cells were treated with 0.1 v/v% HI infusion for 6 h and 24 h or sterile water in triplicates. Equal amounts of RNAs from each sample were hybridized to Human Clariom™ S GeneChip.

first: Katja

last: Kramberger

first: Darja

last: Barlič-Maganja

first: Zala

last: Pražnikar

first: Jure

first: Tadeja

last: Režen

first: Damjana

last: Rozman

first: Saša


title: Epstein-Barr Virus Nuclear Antigen 1 (EBNA1)

city: Madison

first: Bill

last: Sugden

state: WI

address: 1111 Highland Ave

institute: University of Wisconsin-Madison

summary: Expression of mRNAs in EBV-positive B-cell strains in the presence or absence of EBNA1 or a mutant of EBNA1 (ΔUR1-EBNA) that is unable to activate transcription.

overall_design: B-cell strains derived from 2 donors (numbers 20 and 27) infected with WT-EBV and ΔEBNA1-EBV and an unrelated third donor infected with EBV carrying ΔUR1-EBNA1.  Each done in biological triplicate. Samples were normalized to the expression of mRNAs in a pool of RNAs from B-cells from donors 20 and 27 infected with ΔEBNA1-EBV

first: Danielle

last: Westhoff Smith


title: Targeting HER2 Exon 20 Insertion-Mutant Lung Adenocarcinoma with a Novel Tyrosine Kinase Inhibitor Mobocertinib

city: New York

first: Han

last: Han

address: 550 First Avenue

institute: NYU Langone Medical Health

summary: No targeted treatments are currently approved for HER2 exon 20 insertion-mutant lung adenocarcinoma patients. Mobocertinib (TAK-788) is a potent irreversible tyrosine kinase inhibitor (TKI) designed to target human epidermal growth factor receptor 2 (HER2/ERBB2) exon 20 insertion mutations. However, the function of mobocertinib on HER2 exon 20 insertion-mutant lung cancer is still unclear. Here we conducted systematic characterization of preclinical models to understand the activity profile of mobocertinib against HER2 exon 20 insertions. In HER2 exon 20 insertion-mutant cell lines, the IC50 of mobocertinib was higher than poziotinib and comparable with or slightly lower than afatinib, neratinib, and pyrotinib. Mobocertinib had the lowest HER2 exon 20 insertion IC50/wild-type (WT) EGFR IC50 ratio, indicating that mobocertinib displayed the best selectivity profile in these models. Also, mobocertinib showed strong inhibitory activity in HER2 exon 20YVMA allograft and patient-derived xenograft models. In genetically engineered mouse models, HER2 exon 20G776>VC lung tumors exhibited a sustained complete response to mobocertinib, whereas HER2 exon 20YVMA tumors showed only partial and transient response. Combined treatment with a second antibody-drug conjugate (ADC) against HER2, ado-trastuzumab emtansine (T-DM1), synergized with mobocertinib in HER2 exon 20YVMA tumors. In addition to the tumor cell autonomous effect, sustained tumor growth control derived from M1 macrophage infiltration and CD4+ T-cell activation. These findings support the ongoing clinical development of mobocertinib (NCT02716116) and provide a rationale for future clinical evaluation of T-DM1 combinational therapy in HER2 exon 20YVMA insertion-mutant lung adenocarcinoma patients. SIGNIFICANCE: This study elucidates the potent inhibitory activity of mobocertinib against HER2 exon 20 insertion-mutant lung cancer and the synergic effect of combined mobocertinib and T-DM1, providing a strong rationale for clinical investigation.

overall_design: RNA sequencing on HER2 exon 20YVMA tumor nodules treated

first: Shuai

last: Li

first: Ting

last: Chen

first: Kwok-Kin

last: Wong


title: A single dose of lysergic acid diethylamide influences gene expression patterns within the mammalian brain [array]

city: Torino

first: Aurora

last: Savino

state: Piemonte

address: via Nizza, 52

country: Italy

institute: Università di Torino

summary: We have undertaken the first comprehensive analysis of gene expression influenced by acute LSD administration in the mammalian brain to elucidate the mechanism of action of this class of drugs. We have identified a number of genes that are predicted to be involved in the processes of synaptic plasticity, glutamatergic signaling and cytoskeletal architecture. Understanding these molecular events will lead to new insights into the etiology of disorders whose behavioral symptoms resemble the temporary effects of hallucinogenic drugs, and also may ultimately result in new therapies.

overall_design: Four rats were administered 1.0 mg/kg LSD i.p., and four rats were simultaneously administered i.p. saline. After 90 min the animals were decapitated. The brains were removed and the prefrontal cortex was dissected. RNA was extracted from the tissue of four animals pooled per treatment group.

first: Charles

last: Nichols

first: Elaine

last: Sanders-Bush


title: HITI and INDEL analysis by next-generation sequencing

city: Santander

first: Lucio

last: Di Filippo

state: Cantabria

address: PCTCAN - Cl. Albert Einstein, 22

institute: IBBTEC

summary: SpCas9 INDEL frequency and HITI was evaluated at the on-target site of guide RNA targeting either the mouse or pig rhodopsin by next-generation sequencing.

sample_organism:
Sus scrofa
Mus musculus

platform_organism:
Sus scrofa
Mus musculus

overall_design: Two gRNA-treated samples of either mouse or pig were used to amplify the gRNA on-target site with forward primer that anneals to the mRho/pRho sequence and two reverse primers, one that anneals to mRho/pRho and the other to DsRed on the donor DNA.

first: Patrizia

last: Tornabene

first: Anna

last: Manfredi

last: Difilippo


title: H3K4me3 in vivo ChIP-Sequencing data [H3K4me3_invivo_PTs_PALM_VDH15]

city: Sabadell

first: Antoni

last: Berenguer-LLergo

address: Parc del Taulí, 1

institute: Parc Taulí Research and Innovation Institute (I3PT)

summary: H3K4me3 profiling of OSCC secondary (2ary) recipient primary tumors (PTs) following in vivo exposure to control (CTRL) or palm oil-enriched (PALM) diet in primary recipient mice

overall_design: H3K4me3 ChIPs of Control Diet and Palm Diet VDH-15 OSCC tumors (tumors obtained from secondary transplant mice; primary recipient mice were fed for 10 days with either Control/Palm oil-enriched diet) were performed in biological triplicates and technical duplicates (control pLKO.1 cells). The aim of this data set was to determine whether H3K4me3 displayed different ChIP profiles upon exposure to a Palm oil-enriched Diet  when compared to the Control Diet; therefore allowing to assess genome wide the H3K4me3  profiles from in vivo OSCC tumors as well as compare them to the previously obtained H3K4me3 ChIP profiles from an in vitro setting (palmitic acid (PA) stimulated cells in culture).

first: Diana

last: Domínguez

first: Inmaculada

last: Hernández

first: Salvador

last: Aznar


title: LSD influences gene expression patterns within the mammalian brain

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Three-dimensional tissue-engineered human skeletal muscle model of satellite cell quiescence

city: durham

first: Nenad

last: Bursac

address: 101 ciemas dr

institute: Duke University

summary: In vivo, satellite cells (SCs) are essential for skeletal muscle repair. However, in vitro investigation of SC function is challenged by isolation-induced SC activation, loss of the native quiescent state, and differentiation to myoblasts. This study applies  tissue-engineered human skeletal muscle to track myoblast deactivation to 3D-SCs, which bear a quiescent phenotype, as well as examine melittin-induced injury response.

overall_design: CD56+ sorted cells from human muscle were expanded for 5 passages (2D) and used to generate 3D engineered muscle (myobundles). After 4 days of 3D growth conditions, myobundles were differentiated for 3 days (d3), 9 days (d9), or melittin-injured at d7 and sampled 2 days post injury (i2) and 5 days post injury (i5). In the myobundle samples (d3,d9,i2,i5),  cells were dissociated from the myobundles before being subjected to single cell RNA-sequencing (scRNA-seq) using the 10x Genomics Chromium technology.

first: Jason

last: Wang

first: Yarui

last: Diao

first: Yu

last: Xiang


title: Topoisomerase 1 activity during mitotic transcription favors the transition from mitosis to G1 [SLAM-seq]

city: Solna

first: Vladislav

last: Kuzin

state: Stockholm

address: Solnavägen 9

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Institute

summary: Using SLAM-seq to capture de novo synthesized polyadenylated RNAs, we quantitated changes in nascent RNA expression, as well as in total RNA expression.

overall_design: SLAM-seq in asynchronous cells and mitotic cells (two different timepoints: mid and late mitosis, 0 and 40 respectively). To enrich mitotic cells, they were blocked in S phase by addition of 2.5mM thymidine (Sigma, T9250) for 19-24h and, after washing with fresh medium, transferred in fresh medium containing 400ng/ml nocodazole (Sigma, M1404) and incubated for ~14h. Mitotic cells were collected and allowed to progress to mid mitotis (0) and late mitosis (40). All experiments were performed in HCT116 and derived cell lines.

first: Anika

last: Wiegard

first: Donald

middle: P

last: Cameron

first: Jan

last: Grosser

first: Michele

last: Ceribelli

first: Rashid

last: Mehmood

first: Roberto

last: Ballarino

first: Francesco

last: Valant

first: Radosław

last: Grochowski

first: Ivana

last: Karabogdan

first: Nicola

last: Crosetto

first: Arne

last: Lindqvist

last: Bizard

first: Fedor

last: Kouzine

first: Toyoaki

last: Natsume

first: Laura

last: Baranello


title: Topoisomerase 1 activity during mitotic transcription favors the transition from mitosis to G1

first: Anna


title: Chronic LSD alters gene expression profiles in the mPFC relevant to schizophrenia [RNA-seq]

first: Aurora

last: Savino

summary:
Chronic administration of lysergic acid diethylamide (LSD) every other day to rats results in a variety of abnormal behaviors. These build over the 90 day course of treatment and can persist at full strength for at least several months after cessation of treatment. The behaviors are consistent with those observed in animal models of schizophrenia and include hyperactivity, reduced sucrose-preference, and decreased social interaction. In order to elucidate molecular changes that underlie these aberrant behaviors, we chronically treated rats with LSD and performed RNA-sequencing on the medial prefrontal cortex (mPFC), an area highly associated with both the actions of LSD and the pathophysiology of schizophrenia and other psychiatric illnesses.
Results: We observed widespread changes in the neurogenetic state of treated animals four weeks after cessation of LSD treatment. QPCR was used to validate a subset of gene expression changes observed with RNA-Seq, and confirmed a significant correlation between the two methods. Functional clustering analysis indicates differentially expressed genes are enriched in pathways involving neurotransmission (Drd2, Gabrb1), synaptic plasticity (Nr2a, Krox20), energy metabolism (Atp5d, Ndufa1) and neuropeptide signaling (Npy, Bdnf), among others. Many processes identified as altered by chronic LSD are also implicated in the pathogenesis of schizophrenia, and genes affected by LSD are enriched with putative schizophrenia genes. Our results provide a relatively comprehensive analysis of mPFC transcriptional regulation in response to chronic LSD, and indicate that the long-term effects of LSD may bear relevance to psychiatric illnesses, including schizophrenia.

overall_design: mRNA profiles of rats' mPFC after chronic treatment with LSD or saline and 3 weeks of discontinuation.

first: David

last: Martin

first: Danuta

last: Marona-Lewicka

middle: E

last: Nichols

first: Charles


title: Expression data from mouse splenic B cells

city: St. Louis

first: Xiao

last: Huang

state: Missouri

address: 4940 Parkview Place, CSRB 7766, Department of Pathology and Immunology

department: Pathology and Immunology

institute: Washington University in St. Louis, School of Medicine

summary: We used microarrays to detail the impact on B cell gene expression program by Zeb2 enhancer deletion

overall_design: B cells were sorted from spleen for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain the impact of Zeb2 enhancer deletion on B cell gene expression signatures.

first: Kenneth

last: Murphy


title: Promoter and enhancer RNAs regulate chromatin reorganization and activation of miR-10b/HOXD locus and neoplastic transformation in glioma [4C-seq]

first: Evgeny

last: Deforzh

state: MA

address: 60 Fenwood Rd, Brigham and Women's Hospital Neurology Department, 9th Floor

department: Neurology

institute: Brigham and Women's Hospital

summary: Using a combination of chromatin capture techniques, ChIP-Seq, single-molecule in situ RNA analysis, and computational analysis of large-scale TCGA datasets, we identified an epigenetic mechanism underlying common activation of HOXD/miR-10b locus in otherwise highly heterogenous glioma brain tumors. We demonstrate for the first time that two remote lncRNAs, one associated with a genomic promoter and another with a newly identified enhancer, cooperatively shape the 3D chromatin structure and looping, leading to the activation of a large gene cluster (12 genes, 110 KB) that includes the regulatory miRNA essential for glioma survival. This work describes a new mechanism contributing to neoplastic transformation in gliomagenesis, and identifies new avenues for therapeutic interventions based on the promoter and enhancer associated regulatory transcripts.

overall_design: We used 4C-Seq technique with HOXD3/HOXD4/miR10b_gene_body as a viewpoint (NlaIII) to characterize the differences in 3D chromatin architecture between tumorigenic adherent glioma cell line (LN229, U251), low-passage glioma-initiating stem-like cells grown as spheroids (GBM8, GBM6, GBM4) and fetal human astrocytes, neuroprogenitors (NPC) in 500 kb HOXD/miR10b TAD domain. Moreover we examined changes in HOXD/miR10b TAD architecture after HOXD-AS2 (promoter)  OR LINC01116 (enhancer) KD in glioma and 'transformed' astrocytes with active LINC01116 (enhancer). Additionally, HOXD/miR10b chromatin architecture was analyzed after the activation of LINC01116 (enhancer RNA) in fetal human astrocytes.


title: Cisplatin induced gene expression in ex vivo primary tumor cells grown in 3D cultures

city: San Francisco

last: Simpson

state: California

address: 1550 4th Street

institute: UCSF

summary: The objective of this study was to use RNAseq to determine baseline gene expression in mouse primary tumor cells grown in a matrix of matigel and growth factors ex vivo, as well as which genes change expression in response to treatment with a platinum-based therapeutic, cisplatin.

overall_design: Examination of gene expression in mouse primary tumor cells from a lung cancer mouse model grown in 3D cultures ex vivo with (2 replicates) and without (2 replicates) cisplatin treatment.

first: Alex

middle: G

last: Lee

first: Alejandro

last: Sweet-Cordero


title: Identification of Ankrd35 as a mediator of cisplatin response in non-small cell lung cancer by in vivo screening of murine tumor derived xenografts

summary: Using a pooled shRNA library, we performed a focused screen of 81 shRNAs selected for involvement in response to chemotherapy in an ex vivo 3D primary tumor cell culture system. Our results establish Ankrd35, a previously uncharacterized ankyrin repeat domain protein, as an important mediator of chemoresistance in vivo.

overall_design: We analyze shRNA abundance at two different timepoints using 4 biological replicates for genes predicted to play a functional role in chemoresistance and re-growth of the tumor after chemotherapy and compare these results to LKR10 cells (a similar murine NSCLC cell line grown in 2D culture) treated in parallel with cisplatin. The first analysis compares untreated groups T1 v. T0 for any in vivo shRNA vulnerabilities in mouse-derived xenografts (MDXs) and LKR10 cells; the second analysis compares cisplatin treated T1 v. untreated T1 groups for chemosensitizers  in MDXs and LKR10 cells..


title: Identification of Ankrd35 as a mediator of cisplatin response in non-small cell lung cancer by ex vivo 3D screening of primary tumor spheroids


summary: Using pooled shRNA libraries, we performed a focused screen of 515 genes selected for involvement in response to chemotherapy. The results of this screen confirmed Notch signaling is important for primary tumor cell survival and the importance of key DNA damage response regulators for platinum-induced damage, including Ercc1. Our results establish Ankrd35, a previously uncharacterized ankyrin repeat domain protein, as an important mediator of chemoresistance in ex vivo cultures.

overall_design: We analyze shRNA abundance at two different timepoints of 25 sample pools using 3 biological replicates for genes predicted to play a functional role in chemoresistance and re-growth after chemotherapy (25 sample pools x 3 replicates) in primary tumor cells grown in 3D ex vivo cultures and compare these results to LKR10 cells a similar murine NSCLC cell line grown in 2D culture (25 sample pools x 1 replicate). The first analysis compares untreated groups T1 v. T0 for ex vivo 3D vulnerabilities; the second analysis compares cisplatin treated T1 v. untreated T1 groups for chemosensitizers.


title: Promoter and enhancer RNAs regulate chromatin reorganization and activation of miR-10b/HOXD locus and neoplastic transformation in glioma

city: Boston


title: Comparison of gene expression in cisplatin resistant tumors to chemonaive tumors from a lung cancer mouse model

summary: Using a mouse model of non-small cell lung cancer driven by activated Kras and loss of p53 (KrasG12D;p53fl/fl), we sought to determine which genes change expression in the bulk tumor after repetitive treatment with cispatin. After tumors were treated multiple times with cisplatin and show no further response, we isolated RNA from tumors treated with cisplatin or a vehicle control (PBS) to determine which genes significantly change in expression in chemoresistant bulk tumors.

overall_design: 5 replicates of two conditions were tested. In one condition, KP mice with tumors were treated with Cisplatin (7mg/kg) once a week for three weeks until tumors were resistant to Cisplatin. Tumors were microdissected and combined for RNA extraction and hybridization to arrays. In the second condition, chemonaive mice were treated with a vehicle control (PBS) and untreated tumors were harvested for RNA extraction and hybridization to arrays. All samples were analyzed relative to a reference control.

first: Yanyan

last: Zheng

first: Zora

last: Modrusan

first: Cecile

last: de la Cruz

first: Erica

last: Jackson


title: RNA-seq of SIRT5-KO cells infected with SARS-CoV-2

status: Public on Nov 10 2021

first: Eric

last: Verdin

address: 1418D WASHINGTON BLVD

institute: Buck institute

summary: We are studying the role of human sirtuin SIRT5 during viral infection with SARS-CoV-2. We performed RNA-sequencing of WT and SIRT5-KO human lung adenocarinoma A549 cells overexpressing ACE2 (A549-ACE2), in infected and mock-infected conditions. . Our analysis revealed that SARS-CoV-2 replication is attenuated in SIRT5-KO cells. In addition, SIRT5-KO cells expressed higher basal levels of innate immunity markers and mounted a stronger antiviral response. Our results indicate that SIRT5 is a proviral factor necessary for efficient viral replication.

overall_design: RNA-sequencing of WT and SIRT5-KO A549-ACE2 cells, mock infected and infected with SARS-CoV-2.

first: Marius

last: Walter


title: Promoter and enhancer RNAs regulate chromatin reorganization and activation of miR-10b/HOXD locus and neoplastic transformation in glioma [ChIP-seq]

overall_design: In order to characterize epigenetic status of HOXD/miR10b genomic we performed ChIP-Seq with H3K27Ac (#4353, Cell Signaling) and H3K27Me3 (#4353, Cell Signaling) in low-passage glioma-initiating stem-like cells grown as spheroids (GBM8) and fetal human astrocytes. To analyse whether CTCF/Rad21 binding changes after HOXD-AS2 or LINC01116 KD in GBM8 and LINC01116 activation in fetal human astrocytes we performed ChIP-Seq CTCF (#3418, Cell Signaling), Rad21 (ab992, Abcam) .


title: Regulation of gene expression by Ankrd35 in LKR10 cells grown in 2D monoculture or as 3D clusters in methylcellulose

summary: The objective of this study was to use RNAseq to determine which gene change in expression when LKR10 cells are grown in monolayers (2D) or methylcellulose on ultra low attachment plates (3D), which prevents attachment of cells to the plate and promotes formation of 3D sphere-like clusters. A secondary objective was to determine whether knockdown of Ankrd35 altered gene expression of specific genes in 2D or 3D.

overall_design: Examination of gene expression in the murine LKR10 cell line with and without knockdown of Ankrd35 in traditional 2D monolayer cultures and in 3D methylcellulose cultures by RNAseq


title: Benchmark Data for scPLATE-Seq

city: Tucson

first: Hongxu

last: Ding

state: AZ

address: The University of Arizona

institute: University of Arizona

summary: Generate benchmark data for scPLATE-Seq

overall_design: Obtain 1 RNA-Seq profile and 192 scRNA-Seq profiles for HEK293 cells, 96 scRNA-Seq profiles for U87 cells as well as 384 scRNA-Seq profiles for U87-3T3 cell mixture.

first: Jeremy

last: Worley

first: Erin

last: Bush

first: Andrea

last: Califano

first: Peter

last: Sims


title: On/Off targets INDEL analysis  by Next Generation Sequencing

first: Lucio

last: Di Filippo

summary: SpCas9 INDEL frequency was evaluated at both the on- and off-target sites of guideRNA targeting either the murine Rhodopsin or Albumin by Next Generation Sequencing. Minimal INDELs were found at the off target sites evaluted, while SpCas9 activity was predominantly on-target.

overall_design: Three gRNA- and 2 scramble control-treated samples of either retina or liver were used to amplify the gRNA on-target and the top 10 off-target sites.

first: Patrizia

last: Tornabene

first: Rita

last: Ferla

first: Anna

last: Manfredi

last: Difilippo


title: Expression of candidate genes by keratinocytes co-cultured with skin commensal

city: Kiel

first: Lucas

last: Moitinho-Silva

address: Rosalind-Franklin-Straße 12

department: nstitute of Clinical Molecular Biology (IKMB)

institute: University of Kiel

summary: To investigate whether skin bacteria might influence the expression of selected genes, we co-cultured human keratinocytes with S. epidermidis, an abundant commensal in human skin and performed RNA sequencing analysis.

overall_design: Keratinocytes were cultured with and without the addition of Staphylococcus epidermidis cultures, six replicates in each group. Host RNA were isolated and RNA-Seq was performed to identify differential expression of selected genes.

first: Hila

last: Emmert

first: Malte

last: Rühlemann

first: Andre

last: Franke

first: Stephan

last: Weidinger


title: Transcriptome analysis of DSS-treated DOK3-deficient and wildtype mouse colonic cells

city: Singapore

first: Alison

last: Lee

address: 20 Biopolis Way

institute: Bioprocessing Technology Institute

summary: How pathogenesis of inflammatory bowel disease (IBD) depends on the complex interplay of host genetics, microbiome and the immune system is not fully understood. Here, we showed that Downstream of Kinase 3 (DOK3), an adaptor protein involved in immune signaling, confers protection of mice from dextran sodium sulfate (DSS)-induced colitis. DOK3-deficiency promotes gut microbial dysbiosis and enhanced colitis susceptibility, which can be reversed by the transfer of normal microbiota from wild-type mice. Mechanistically, DOK3 exerts its protective effect by suppressing JAK2/STAT3 signaling in colonic neutrophils to limit their S100a8/9 production, thereby maintaining gut microbial ecology and colon homeostasis. Hence, our findings reveal that the immune system and microbiome function in a feed-forward manner, whereby DOK3 maintains colonic neutrophils in a quiescent state to establish a gut microbiome essential for intestinal homeostasis and protection from IBD.

overall_design: Colonic cells were isolated from wildtype and Dok3-deficient mice before and six days after dextran sulfate sodium (DSS) challenge (n=4 each).

first: Jia

middle: T

last: Loh

first: Koon

first: Kong-Peng

last: Lam


title: Transcriptome study of the deletion of vacuolar protein sorting related vps13 and vps21 in Trichoderma reesei

city: 无锡

first: 肃

last: 闫

state: 江苏

address: 江苏省无锡市滨湖区江南大学生物工程学院

institute: Jiangnan University

summary: The disruption of vacuolar protein sorting related genes vps13 and vps21 in filamentou fungi Trichoderma reesei resulted in a dramtic increase in cellulase transcription especially in the late Avicel induction phase, relieving the RESS (REpression under Secretion Stress) effect. Great interest arisen concered about the reason and underlying mechanism of vps13 and vps21 disruption for increased cellulase transcription. Thus, transcriptome analysis through RNA-Seq could give a deep insight of the potential pathways involved in enhanced cellulase transcription in late Avicel induction.

overall_design: Mycelia sampled of wild type, and its vps mutant Δvps13 and Δvps21, from Avicel induction medium at day 4 were conducted for RNA-Seq

first: Su

last: Yan

first: Xiao-Wei

last: Yu


title: A Phase I, Open-Label, Dose-Escalation Study of the OX40 Agonist Ivuxolimab in Patients With Locally Advanced or Metastatic Cancers

city: Houston

first: David

last: Hong

state: TX

address: 1515 Holcombe Boulevard Unit 455

institute: University of Texas M.D. Anderson Cancer Center

summary: Gene sets enriched in tumor tissue in response to dosing with ivuxolimab from eight paired biopsies of patients dosed with ≥ 1.5 mg/kg indicated that gene sets associated with immune activation and inflammation were among those most enriched (higher positive normalized enrichment score [NES]) with the lowest adjusted P values.

overall_design: Whole transcriptome sequencing of paired (pre/post-dose) tumor samples from patients treated with ≥ 1.5 mg/kg of ivuxolimab. Whole transcriptome sequencing was performed by Personalis using ACE ImmunoID assay.

first: Bishu

last: Ganguly

first: Catherine

last: Fleener

first: Xiao

last: Wang


title: Allelic variation in Class I HLA determines pre-existing memory responses to SARS-CoV-2 that shape the CD8+ T cell repertoire upon viral exposure

first: Natalie

middle: Y. R.

last: Agar

state: Massachusetts

address: Harvard Medical School

department: Neurosurgery

summary: Effective presentation of antigens by HLA class I molecules to CD8+ T cells is required for viral elimination and generation of long-term immunological memory. In this study, we applied a single-cell, multi-omic technology to generate the first unified ex vivo characterization of the CD8+ T cell response to SARS-CoV-2 across 4 major HLA class I alleles. We found that HLA genotype conditions key features of epitope specificity, TCR a/b sequence diversity, and the utilization of pre-existing SARS-CoV-2 reactive memory T cell pools. Single-cell transcriptomics revealed functionally diverse T cell phenotypes of SARS-CoV-2-reactive T cells, associated with both disease stage and epitope specificity. Our results show that HLA variations significantly influence the CD8+ T cell repertoire shape and utilization of immune recall upon SARS-CoV-2 infection.

overall_design:
We performed analysis of CD8+ T cell responses in PBMCs from three cohorts - acute COVID, convalesecent COVID, and unexposed subjects. Single-cell sequencing was used for quantification of mRNA expression, tetramer binding, and ADT binding.
Some samples were multiplexed with cell hashing. The metadata and hashtog barcode oligo sequence for each hashed sample is included in the file GEO_upload_seq_CIPHER_2021_11_04_Supplemental_Sample_to_HTO.xlsx, available at the foot of this record.

first: J

last: Francis

first: D

last: Leistritz-Edwards


title: A single-cell culture system for dissecting microenvironmental signaling in development and disease of cartilage tissue

city: Los Angeles

first: Denis

last: Evseenko

address: 1450 Biggy St

department: Orthopaedic Surgery

institute: University of Southern  California

summary: Cartilage tissue is comprised of extracellular matrix and chondrocytes, a cell type with very low cellular turnover in adults, providing limited capacity for regeneration. However, in development a significant number of chondrocytes actively proliferate and remodel the surrounding matrix. Uncoupling the microenvironmental influences that determine the balance between clonogenic potential and terminal differentiation of these cells is essential for the development of novel approaches for cartilage regeneration. Unfortunately, most of the existing methods are not applicable for the analysis of functional properties of chondrocytes at a single cell resolution. Here we demonstrate that a novel 3D culture method provides a long-term and permissive in vitro niche that selects for highly clonogenic, colony-forming chondrocytes which maintain cartilage-specific matrix production, thus recapitulating the in vivo niche. As a proof of concept, clonogenicity of Sox9IRES-EGFP mouse chondrocytes is almost exclusively found in the highest GFP+ fraction known to be enriched for chondrocyte progenitor cells. Although clonogenic chondrocytes are very rare in adult cartilage, we have optimized this system to support large, single cell-derived chondrogenic organoids with complex zonal architecture and robust chondrogenic phenotype from adult pig and human articular chondrocytes. Moreover, we have demonstrated that growth trajectory and matrix biosynthesis in these organoids respond to a pro-inflammatory environment. This culture method offers a robust, defined and controllable system that can be further used to interrogate the effects of various microenvironmental signals on chondrocytes, providing a high throughput platform to assess genetic and environmental factors in development and disease.

overall_design: mRNA sequencing for SOX9-GFP (postnatal day7) chondrocytes from mouse

first: Ben

last: Van Handel


title: Low-input, deterministic profiling of single-cell transcriptomes reveals individual intestinal organoid subtypes comprised of single, dominant cell types [Intestinal crypts]

city: Lausanne

first: Marjan

last: Biočanin

state: Vaud

address: Station 19, SV 3820

department: SV-IBI

institute: EPFL

summary: High-throughput single-cell RNA-sequencing (scRNA-seq) has transformed our ability to resolve cellular properties across systems. A key scRNA-seq catalyzer was the introduction of microdroplet-based systems, which vastly improved sample handling and cell throughput. While powerful, the current microfluidic systems are limited to high cell density (>1000 cells) samples. This prevents the efficient processing of individual, small tissues or rare cells, leading to respectively confounded mosaic cell population read-outs or failed capture of diagnostically interesting cells.  In this study, we developed a deterministic, mRNA-capture bead and cell co-encapsulation droplet system, DisCo, that overcomes these limitations by enabling precise particle position and droplet sorting control through combined machine-vision and multilayer microfluidics. We demonstrate that DisCo is capable of processing samples containing few cells (< 100 cells) at high efficiencies( >70%). To underscore the unique capabilities of DisCo, we mapped the developmental process of 31 individual intestinal organoids at the single cell level. This uncovered extensive cellular heterogeneity among organoids, revealing two so far uncharacterized organoid subtypes, “gobloids” and spheroids, predominantly consisting of respectively Muc2+ goblet and Ly6a+ stem cells. Further Disco data analysis thereby revealed strongly increased Yap1 target gene expression in these spheroids, suggesting mechano sensing as the underlying mechanism for their spontaneous formation.  Together, our novel “no-cell-left-behind” platform enables the deterministic processing of input cells, allowing high-resolution snapshots of cellular heterogeneity among rare cells or individual, small tissues or organoids.Together, our novel “no-cell-left-behind” platform enables the deterministic processing of input cells, allowing high-resolution snapshots of cellular heterogeneity among rare cells or individual, small tissues or organoids.

overall_design: Crypts were isolated from single small intestines of 7-week old male C57BL/6J mice following the protocol from Bas and Augenlicht et al. Briefly, the small intestine of one mouse was isolated and then washed both on the inside and outside with ice cold PBS. The small intestine was cut open longitudinally and washed again with PBS. The intestine was then non-enzymatically digested for 3 minutes in PBS/EDTA/DTT. Next, the tissue was cut into small pieces and transferred into a 50 mL Falcon tube containing 20 mL of ice-cold PBS. The PBS solution containing the tissue pieces was gently triturated 10 times using a 10 mL pipette. After tissue fragments had sedimented, the supernatant was removed, and the process was repeated three more times until the supernatant was clear. Next, the supernatant was removed, PBS/EDTA was added and the sample incubated for 30 minutes at 4oC on a rocking plate. After incubation, tissue fragments were left for sedimentation (up to 5 minutes), then the supernatant was removed. Subsequently, tissue fragments were triturated with ice cold PBS by pipetting up and down. After large tissue fragments sedimented (up to 5 minutes), the supernatant containing crypts was collected as Fraction 1 (F1). Fraction collection was repeated five times (F2-F5), followed by trituration with ice cold PBS, while each fraction was stored separately. Each fraction was inspected for cell debris and villus contamination.For single-cell bulk sample preparation, crypts from F2 or F3 were spun down at 600 x g for 10 minutes (brake 5). Following centrifugation, the supernatant was removed and cells were enzymatically dissociated for 1 minute at 37oC. Cells were then washed two times in PBS/BSA and strained two times using a Flowmi 40 µm strainer to minimize the doublet rate. Cell suspensions were diluted in cell loading buffer and applied to the loading tip connected to the DisCo chip. For single-cell isolation from single crypts, crypts from F3 were transferred to FBS coated 6 well plates. Subsequently, single crypts were isolated by hand-picking after which they were transferred to a Nunc microwell culture plate containing single crypt dissociation mix. Single crypts were dissociated by combining trituration using non-filter pipette tips every 5 minutes and incubation at 37oC for a total of 15 minutes. Following dissociation, cell suspensions were diluted in cell loading buffer and applied to the loading tip connected to the DisCo chip.

first: Johannes

last: Bues

first: Joern

last: Pezoldt

first: Riccardo

last: Dainese

first: Antonius

last: Chrisnandy

first: Saba

last: Rezakhani

first: Wouter

last: Salen

first: Revant

last: Gupta

first: Esther

last: Amstad

first: Manfred

last: Claassen

first: Matthias

last: Lutolf

first: Bart

last: Deplancke


title: Low-input, deterministic profiling of single-cell transcriptomes reveals individual intestinal organoid subtypes comprised of single, dominant cell types [split organoids]

overall_design: Organoids for the split organoid experiment were cultured as previously described.20 Single organoids, derived from Days 2 – 6 post splitting were isolated from Matrigel as described above. The single cell suspension of one organoid was split into two separate samples, and introduced subsequently on the system.


title: Sorted HSCs from aged Specific Pathogen Free and germ free mice

city: Saint Louis

first: Daniel

last: Link

state: MO

address: 660 S. Euclid Avenue

department: Oncology

institute: Washington University in St. Louis

summary: To begin to explore mechanisms by which microbiota signals regulate HSC lineage bias, gene expression profiling was performed on sorted LSK-SLAM cells from aged SPF and aged GF mice.

overall_design: 2ng of HSC total RNA was amplified from 3 aged SPF mice and 3 aged GF mice

first: Joseph

last: Krambs

first: Darlene

middle: A

last: Monlish

first: Feng

last: Gao

first: Laura

last: Schuettpelz


title: RACK1 prevents premature differentiation of epidermal progenitors by inhibiting IRF6 expression

city: La Jolla

first: George

last: Sen

address: 9452 Medical Center Dr

department: Dermatology

institute: University of Californai San diego

summary: To continuously maintain barrier function, skin progenitor cells perpetually proliferate and differentiate to contribute to the outermost layers. Perturbations in the balance between stem cell self-renewal and differentiation leads to a variety of disorders. Thus, it is critical to identify the factors that govern progenitor cell fate decisions. Here, we show RACK1 (GNB2l1) to be necessary to maintain epidermal progenitor cell self-renewal by transcriptionally repressing IRF6, a transcription factor critical for epithelial differentiation program initiation.

overall_design: RNAseq analysis of human epidermal progenitor cells transfected with shRNA against RACK1 and Ctr.  RNA sequenced in replicates.

first: Ji

last: Ling


title: Low-input, deterministic profiling of single-cell transcriptomes reveals individual intestinal organoid subtypes comprised of single, dominant cell types [HEK Kinetic]

first: Marjan

last: Biočanin

overall_design: A single-cell suspension of HEK 293T (ATCC Cat. No. SD-3515) was loaded on the system as described above, and the remaining volume stored on ice. To evaluate the temporal batch effect, cells were sampled from the same prepared suspension. After 20 minutes, droplets were evacuated from the system and sequencing libraries prepared. A new cell loading tip was inserted into the sample outlet port and the experimental run was resumed. The previous steps were repeated after 40 and 60 minutes. After 120 minutes, the system was loaded with cells stored on ice and cells captured for approximately 20 minutes. Subsequently, droplets were evacuated from the system, cDNA was generated, and sequencing libraries prepared as described above. The former steps were repeated 180 minutes from the first DisCo experiment.

first: Johannes

last: Bues

first: Joern

last: Pezoldt


title: Carboplatin-mediated recovery of LPS-induced tolerant macrophages via H3K9me3 modifications

city: Bangkok

first: Tanapat

last: Palaga

address: Payathai Road, Pathumwan

department: Microbiology

country: Thailand

institute: Chulalongkorn University

summary: Following the re-exposure to lipopolysaccharide (LPS), macrophages exhibit the immunosuppressive state contribute to low production of proinflammatory cytokines and inability to respond the stimuli, a phenomenon is termed “tolerance”. Histone modification has been found in LPS-induced tolerant macrophages. Carboplatin, an antitumor drug, exerts its general effect on inhibition of DNA replication and transcription as well as epigenetic modification. Therefore, we hypothesized that carboplatin can be used to rescue the tolerance in macrophages. We found that carboplatin increases IL-6 but not TNF-α production in LPS-primed cells. The significant inductions were examined in carboplatin-treated tolerant macrophages evaluated by ELISA and qPCR. GSEA analyses revealed that p53 was the significant hallmark in both primed and tolerant RNA-Seq transcripts under carboplatin exposure while E2F ang G2/M were the upmost in negative hallmarks. HP1-α, heterochromatin protein 1, was significantly reduced in carboplatin-treated tolerant macrophages. The significant lower transcript of H3K9me3 methyltransferase, setdb2, was determined whereas kdm4d, demethylase encoding gene was significantly up-regulated in the presence of carboplatin in tolerant macrophages. Based on our data we suggested that carboplatin mediated upregulation of proinflammatory cytokine and rescue tolerance via the H3K9me3 modification. Carboplatin is potentially be a therapeutic drug for tolerance recovery in sepsis patients.

overall_design: Bone marrow-derived macrophages (BMDM)s mRNA profile of untreated controls, primary LPS-stimulated cells, LPS-primed cells treated with carboplatin, LPS-induced tolerant cells, tolerant cells with carboplatin, and single LPS control cells. All experiments were performed in triplicates.

first: Atsadang

last: Boonmee

first: Salisa

last: Benjaskulluecha

first: Patipark

last: Kueanjinda

first: Benjawan

last: Wongprom

first: Thitiporn

last: Pattarakankul


title: Resolving monocytes generated through TRAM deletion attenuate the pathogenesis of atherosclerosis

city: Blacksburg

first: Liwu

last: Li

state: VA

address: 1015 Life Science Cir

institute: Virginia Tech

summary: We performed scRNAseq analysis of murine monocytes cultured from bone marrow isolates of WT and TRAM knockout mice. WT and TRAM knockout monocytes were cultured in vitro for 5 days in the presence or absence of low dose LPS (100 pg/ml).

overall_design: Monocytes isolated from C57BL/6 WT mice were cultured with low dose LPS (100 pg/ml) or PBS control for 5 days. Likewise, Tram-deficient monocytes were harvested from TRAM KO mice and cultured for 5 days with 100 pg/ml LPS or control PBS.

first: Ziyue

last: Yi

first: Shuo

last: Geng


title: Analysis of genes of different expression in gastric cancer cells between ARV-825 treatment group and control group.

city: Shanghai

first: Xinmei

last: Liao

state: Shanghai

address: 800 Dongchuan RD

department: department of instrument science and engineering

institute: Shanghai Jiao Tong University

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analyze genes of different expression in gastric cancer cells between arv-825 treatment group and control group and to evaluate protocols for optimal high-throughput data analysis

overall_design: mRNA profiles in gastric cancer cells of arv-825 treatment group and control group were generated by deep sequencing, in triplicate, using Illumina GAIIx.


title: RNA-Seq analysis of human MEN1-associated thymic carcinoid and thymoma compared to normal thymus

city: Bethesda

first: Sunita

last: Agarwal

state: MD

address: Bldg. 10, Room 8C101

department: NIDDK

institute: National Institutes of Health

summary: RNA-Sequencing was performed on rRNA-depleted RNA samples that were isolated from formalin fixed paraffin embedded (FFPE) tissue sections of human normal thymus and human thymic tumors of patients with multiple endocrine neoplasia type 1 (MEN1) syndrome.

overall_design: RNA-Seq of 11 thymic carcinoids and 2 thymoma from MEN1 patients was compared to the RNA-Seq of 6 normal thymus.

first: Adel

last: Mandl


title: The potential mechanism of ankylosing spondylitis

city: hefei，anhui，china

first: jian-xiong

last: wang

state: anhui

address: No. 218，Ji-xi Road，Hefei 230022, Anhui, China.

institute: Hospital

summary: Whole blood RNA-sequencing data from 5 AS patients who met 1984 AS criteria and 3 healthy human were obtained to gain insight into the potential mechanism of ankylosing spondylitis.

overall_design: Whole blood RNA-sequencing data from 5 AS patients who met 1984 AS criteria and 3 healthy human were obtained.

first: Sheng-qian

last: Xu

first: Jian-xiong

last: Wang

first: He-xiang

last: Zong

first: Yi-ran

last: Chu


title: Deletion of Abi3 gene locus exacerbates neuropathological features of Alzheimer’s disease in a mouse model of Aβ amyloidosis

city: Indianapolis

first: Jungsu

last: Kim

state: IN

address: 320 W. 15th Street

institute: Indiana University School of Medicine

summary: Recently, large-scale human genetics studies identified a rare coding variant in the ABI3 gene that is associated with an increased risk of late-onset Alzheimer’s disease (AD). However, pathways by which ABI3 contributes to the pathogenesis of AD are unknown. To address this critical question, we determined whether loss of ABI3 function affects pathological features of AD in the 5XFAD mouse model. We demonstrate that the deletion of Abi3 locus significantly increases amyloid-b (Ab) accumulation and decreases microglia clustering around the plaques. Furthermore, long-term potentiation is impaired in 5XFAD;Abi3 knock-out (“Abi3-/-”) mice. Moreover, we identified dramatic changes in the proportion of microglia subpopulations in Abi3-/- mice using a single-cell RNA sequencing approach. Mechanistic studies demonstrate that Abi3 knockdown in microglia impairs migration and phagocytosis. Taken together, our study provides the first in vivo functional evidence that loss of ABI3 function may increase the risk of developing AD by affecting Ab accumulation and neuroinflammation.

overall_design: Quant-seq (3' mRNA-seq) analysis of cerebral cortices of female 5xFAD mice with Abi3 +/+ (Abi3 WT) or Abi3 -/- (Abi3 KO) genotypes at 8 months of age

first: Hande

last: Karahan

first: Daniel

last: Smith

first: Byungwook

first: Luke

last: Dabin

first: M

middle: M

last: Al-Amin

first: H

last: Wijeratne

first: Taylor

last: Pennington

first: Gonzalo

middle: V

last: di Prisco

first: Brianne

last: McCord

first: Peter

middle: B

last: Lin

first: Yuxin

first: Junmin

last: Peng

first: Adrian

last: Oblak

first: Shaoyou

first: Brady

last: Atwood


title: Low-input, deterministic profiling of single-cell transcriptomes reveals individual intestinal organoid subtypes comprised of single, dominant cell types [C1-HEK]

first: Marjan

last: Biočanin

overall_design: To benchmark the cell recovery efficiency of the Fluidigm C1 platform, HEK 293T (ATCC Cat. No. SD-3515) cells were diluted to reach approximately 10, 20, 40 cells per µL.12 µL of cell solution was mixed with 8 µL of Suspension Reagent from Fluidigm. The obtained suspensions were generated separately from the same stock and then quantified in triplicate using microscopy by examining a volume of 2 x 2.5 µL of the suspension between two coverslips. Counts of all triplicates were averaged to estimate the cell input for 5 µL of Cell Mix to the C1 IFC. The experiment on the C1 machine was performed according to the kit’s manual: “SMART-Seq v4 Ultra Low Input RNA Kit for the Fluidigm C1 System, IFCs User Manual” (Clontech Laboratories, Inc.) using 10 – 17 µm 96-trap trap C1 IFC OpenApp chips. The prrotocol was run on SMART-Seq v4 (1861x/1862x/1863x) programs on the C1 machine. To verify successful loading and cell trapping, a Cell xCellence (Olympus) microscope was used. Final cDNA was quantified using the PicroGreen dsDNA assay and then tagmented using a Nextera XT kit.

first: Johannes

last: Bues

first: Joern

last: Pezoldt

first: Riccardo

last: Dainese

first: Antonius

last: Chrisnandy

first: Saba

last: Rezakhani

first: Wouter

last: Salen

first: Revant

last: Gupta

first: Esther

last: Amstad

first: Manfred

last: Claassen

first: Matthias

last: Lutolf

first: Bart

last: Deplancke


title: Development of gene expression signatures for BV-2 microglia activation in the background of mild hypothermia

city: Hefei

first: Jiagen

last: Wen

state: Anhui

address: NO.81, Meishan Road, Anhui Medical University

institute: Anhui Medical University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Sepsis associated encephalopathy (SAE), a common complication of sepsis, seriously affect the prognosis and quality of life to sepsis patients. Microglia activation is vital to the neuroinflammation and the pathology of SAE. Mild hypothermia, that a useful procedure in the treatment of traumatic brain injuries, was found to suppress microglia activation. In present study, in vitro cultured BV-2 microglial cells stimulated with LPS was employed as the model of microglia activation. The altered signitures of lncRNAs, circRNAs and mRNAs of LPS exposure and mild hypothermia were arrayed by using the Agilent ceRNA Microarray Chip.

overall_design: BV-2 cells were divided into four group: mild hypothermia (33◦C), mild hypothermia (33◦C) and lipopolysaccharide (1000ng/ml), normal temperature (37◦C), normal temperature (37◦C) and lipopolysaccharide(1000ng/ml). The experiment repeated for three time.

first: Qilian

last: Xie


title: Hi-C sequencing data of WT and Zeb2 enhancer mutant splenic CD8+ T cells

city: St. Louis

first: Xiao

last: Huang

address: 4940 Parkview Place, CSRB 7766, Department of Pathology and Immunology

institute: Washington University in St. Louis, School of Medicine

summary: To evaluate the impact of -165-kb Zeb2 enhancer deletion on 3D chromatin structure, we performed in situ Hi-C analysis of WT and Zeb2 –165–/– splenic CD8+ T cells, which showed no significant global changes on the structure of chromosome 2

overall_design: Examination of overall chromatin structure of WT and Zeb2 enhancer mutant splenic CD8+ T cells.

first: Kenneth

last: Murphay


title: RNA-sequencing of human pluripotent stem-cell derived endothelial cells under control and Wnt-activating conditions

first: Benjamin

last: Gastfriend

state: CA

address: 9500 Gilman Dr

institute: University of California, San Diego

summary: Endothelial cells (ECs) in the central nervous system (CNS) acquire specialized barrier properties in response to extrinsic signals, with Wnt/β-catenin signaling coordinating multiple aspects of endothelial barrier function. We used human pluripotent stem cell (hPSC)-derived endothelial progenitor cells to profile the EC response to Wnt activation using multiple strategies, including the small molecule GSK-3 inhibitor CHIR 99021, and the CNS-derived ligands Wnt7a and Wnt7b.

overall_design: 20 total samples were analyzed, 18 endothelial cell (EC) samples and 2 smooth muscle-like cell (SMLC) samples. All cells were differentiated from the human induced pluripotent stem cell line iPS(IMR90)-4. Four independent differentiations were performed (denoted 2, 3, 5, and 6). At Passage 1, ECs treated with DMSO (vehicle control), 4 uM CHIR 99021 (CHIR), or 50 ng/ml each Wnt7a and Wnt7b (WNT) were analyzed from differentiations 2, 3, 5, and 6. At Passage 3, ECs treated with DMSO or CHIR were analyzed from differentiations 2, 3, and 6. At Passage 1, SMLCs treated with DMSO were analyzed from differentiations 3 and 6. For Passage 1 samples, fluoresence-activated cell sorting was used to isolate CD31+ (EC) and CD31- (SMLC) populations.

first: Sean

last: Palecek

first: Eric

last: Shusta


title: IFNg is Critical for CAR T Cell Mediated Myeloid Activation and Induction of Endogenous Immunity

city: Duarte

first: Hsun

middle: Teresa

last: Ku

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

summary: Chimeric antigen receptor (CAR) T cells mediate potent antigen-specific antitumor activity, however, their indirect effects on the endogenous immune system is not well characterized. Remarkably, we demonstrate that CAR T cell treatment of mouse syngeneic glioblastoma activates intratumoral myeloid cells and induces endogenous T cell memory responses coupled with feed-forward propagation of CAR T responses. IFNγ production by CAR T cells and IFNγ-responsiveness of host immune cells is critical for tumor immune landscape remodeling to promote a more activated and less suppressive tumor microenvironment. The clinical relevance of these observations is supported by studies showing that human IL13Rα2-CAR T cells activate patient-derived endogenous T cells and monocyte/macrophages through IFNg-signaling, as well as induce the generation of tumor-specific T cell responses in a responding patient with GBM. These studies establish that CAR T therapy has the potential to shape the tumor microenvironment, creating a context permissible for eliciting endogenous antitumor immunity.

overall_design: CD45+ cells were sorted from untreated or CAR-T cell treated KR158-Luc tumor bearing mouse brains, 3 days after adoptive transfer and sequenced on the 10x Genomics platform

first: Darya

last: Alizadeh

first: Robyn

last: Wong

first: Min-Hsuan

last: Chen

first: Xiwei

last: Wu


title: CsHEC2 regulates fruit wart formation through interaction with CsGL3 and CsTu and directly promoting cytokinin biosynthesis in cucumber

city: Beijing

first: zhongyi

last: wang

state: Beijing

address: No.2 Yuanmingyuan Xi Lu

institute: CAU(China Agricultural University)

summary: Cucumber fruit wart composed of spine and tubercule is an important appearance quality trait, which affects product classification and market value of cucumber fruit. Although several key genes for initiation and development of spine and tubercule have been cloned, their underlying mechanisms and relationships have not been well studied. Here, we identified a cucumber basic Helix-Loop-Helix (bHLH) gene CsHEC2 that was strongly expressed in spines and tubercules of cucumber peel. Knockout lines obtained using CRISPR/Cas9 technology were used to explore the biological function of CsHEC2. Compared with the wild type, the Cshec2 mutants resulted in reduced density of wart, and decreased cytokinin accumulation in fruit peel compared to wild type. To comprehensively analyze the regulatory network, RNA sequencing (RNA-seq) experiments were conducted on female buds at 7 days before anthesis (DBA). Transcriptomic data analysis showed that 293 and 1295 genes were up- and down-regulated in Cshec2 mutants relative to WT, respectively. Several sets of genes for cytokinin biosynthesis and metabolism were expressed differently, which explained the decrease of cytokinin in Cshec2 mutants. Our results suggested that CsHEC2 is very likely to regulate the initiation of fruit wart by affecting cytokinin pathway.

overall_design: RNA sequencing experiments were performed using the female buds at 7 days before anthesis. Samples were obtained from WT and Cshec2 mutant lines, and three biological replicates were set for each sample.

first: Zhongyi

last: Wang

first: Liming

first: Lijie

last: Han

first: Zhihua

last: Cheng

first: Xiaofeng

last: Liu

first: Liu

first: Jiacai

first: Weiyuan

last: Song

first: Zhaoyang

last: Zhou

first: Xiaolan

last: Zhang


title: Next Generation Sequencing Facilitates Quantitative Analysis of Vehicle Control and Vismodegib Treated Tumor Transcriptomes II

city: Birmingham

first: Dongquan

state: AL

address: 1717 11th Ave South

department: Medicine

institute: Univ of Alabama at Birmingham

summary: Purpose:  The goal of this study is to compare transcriptome profiling (RNA-seq) between tumors of mammary tumor bearing mice treated with a vehicle control or FDA approved Hedgehog signaling inhibitor, Vismodegib.

overall_design: Methods: mRNA profiles of vehicle control and Vismodegib treated mice were generated by deep sequencing, using Illumina HiSeq. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS).

first: Dominique

last: Hinshaw

first: Tesh

last: Sherpa


title: Hi-C2 of mouse splenic macrophages and pDCs

city: SAINT LOUIS

first: Daofeng

last: Li

address: 4515 McKinley Avenue

department: Genetics

summary: The transcriptional repressor Zeb2 regulates development of many cell fates among somatic, neural and hematopoietic lineages, but the basis for its requirement in these diverse linages is unclear. Our recent study uncovered a mutually repressive regulatory circuit between Id2 and Zeb2, and predicted that Zeb2 should be positively regulated by members of the E protein family of transcription factors. Here, we identified a 400bp enhancer region located 165 kilobases (kb) upstream of the Zeb2 transcriptional start site (TSS) that binds the E proteins E2A and E2-2 at several E-box motifs and is active in hematopoietic lineages. Germline deletion of this 400bp region (Zeb2 –165–/– mice) specifically prevented Zeb2 expression in hematopoietic stem cell (HSC) derived lineages. Zeb2 –165–/– mice lacked development of pDCs, monocytes, and B cells. Surprisingly, all macrophages in Zeb2 –165–/– mice were exclusively of embryonic origin. Using single-cell chromatin profiling, we identified a second Zeb2 enhancer located at +164kb that is selectively active in embryonically derived lineages, but not in lineages derived from HSCs. Thus, Zeb2 expression in adult, but not embryonic, hematopoiesis is selectively controlled by the –165kb Zeb2 enhancer.

overall_design: Hi-C2 on: splenic macrophages (2 biological replicates) and pDCs (3 biological replicates) sorted from WT B6 mice; splenic macrophages (2 biological replicates) sorted from Zeb2-165-/- B6 mice

first: Mayank

middle: N

last: Choudhary

first: Changxu

last: Fan

first: Ting